ELAV Intron 8: a single-copy sequence marker for shallow to
deep phylogeny in Eupulmonata Hasprunar & Huber, 1990 and
Hygrophila Ferussac, 1822 (Gastropoda: Mollusca)

J 2023

ELAV Intron 8: a single-copy sequence marker for shallow to deep phylogeny in Eupulmonata Hasprunar & Huber, 1990 and Hygrophila Ferussac, 1822 (Gastropoda: Mollusca)

NEKOLA, Jeffrey Clark, Markéta NOVÁKOVÁ, Michal HORSÁK a Coen M. ADEMA

Základní údaje

Originální název

ELAV Intron 8: a single-copy sequence marker for shallow to deep phylogeny in Eupulmonata Hasprunar & Huber, 1990 and Hygrophila Ferussac, 1822 (Gastropoda: Mollusca)

Autoři

NEKOLA, Jeffrey Clark (840 Spojené státy, garant, domácí), Markéta NOVÁKOVÁ (203 Česká republika, domácí), Michal HORSÁK (203 Česká republika, domácí) a Coen M. ADEMA

Vydání

Organisms Diversity and Evolution, Springer, 2023, 1439-6092

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10602 Biology , Evolutionary biology

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 1.600 v roce 2022

Kód RIV

RIV/00216224:14310/23:00134096

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1007/s13127-022-00587-3

UT WoS

000878936100001

Klíčová slova anglicky

PCR; nDNA; Intron; Phylogenetic marker; Gastropods

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 20. 2. 2024 09:11, Mgr. Marie Šípková, DiS.

Anotace

V originále

Progress in eupulmonate gastropod taxonomy is limited by absence of single- or low-copy nuclear DNA markers that provide species-scale insights. We detail here the single-copy intron 8 of the embryonic lethality and abnormal visual system gene (ELAVI8). High sequence conservation within flanking exons 8 and 9 allowed design of non-redundant primers that enable PCR amplification across a broad phylogenetic extent. Across the Eupulmonata and Hygrophila ELAVI8 product ranged from 602 to 802 base pairs in length. A multiple sequence alignment across 62 taxa, representing 36 genera and 12 major clades, showed 1296 sites with 865 variable positions. Typically, 2-10 base pair differences were noted between closely related species within a genus, with 74-200 bases differing between major infra-order clades. ELAVI8 maximum-likelihood trees showed essentially identical topologies at high levels of support compared to those created from concatenated ITS1 + 2 (within a genus) or 28S (across Eupulmonata and Hygrophila). ELAVI8 is superior to these two phylogenetic marker regions, however, because it (1) resolves phylogenetic pattern from species- to sub-cohort scales in a single amplicon, (2) was better able to resolve family- and deeper-clades at high support, (3) allows for outgroup rooting between genera, and (4) possesses no intercopy haplotype variability.

Návaznosti

GA22-23005S, projekt VaV

Název: Identifikace a optimalizace nových úseků jaderné DNA pro fylogenetickou analýzu plicnatých plžů na druhové úrovni

Investor: Grantová agentura ČR, Identifikace a optimalizace nových úseků jaderné DNA pro fylogenetickou analýzu plicnatých plžů na druhové úrovni

Citovat

NEKOLA, Jeffrey Clark, Markéta NOVÁKOVÁ, Michal HORSÁK a Coen M. ADEMA. ELAV Intron 8: a single-copy sequence marker for shallow to deep phylogeny in Eupulmonata Hasprunar & Huber, 1990 and Hygrophila Ferussac, 1822 (Gastropoda: Mollusca). Organisms Diversity and Evolution. Springer, 2023, roč. 23, č. 3, s. 621-629. ISSN 1439-6092. Dostupné z: https://dx.doi.org/10.1007/s13127-022-00587-3.

@article{2271920,
   author = {Nekola, Jeffrey Clark and Nováková, Markéta and Horsák, Michal and Adema, Coen M.},
   article_number = {3},
   doi = {http://dx.doi.org/10.1007/s13127-022-00587-3},
   keywords = {PCR; nDNA; Intron; Phylogenetic marker; Gastropods},
   language = {eng},
   issn = {1439-6092},
   journal = {Organisms Diversity and Evolution},
   title = {ELAV Intron 8: a single-copy sequence marker for shallow to deep phylogeny in Eupulmonata Hasprunar & Huber, 1990 and Hygrophila Ferussac, 1822 (Gastropoda: Mollusca)},
   url = {https://doi.org/10.1007/s13127-022-00587-3},
   volume = {23},
   year = {2023}
}

TY  - JOUR
ID  - 2271920
AU  - Nekola, Jeffrey Clark - Nováková, Markéta - Horsák, Michal - Adema, Coen M.
PY  - 2023
TI  - ELAV Intron 8: a single-copy sequence marker for shallow to deep phylogeny in Eupulmonata Hasprunar & Huber, 1990 and Hygrophila Ferussac, 1822 (Gastropoda: Mollusca)
JF  - Organisms Diversity and Evolution
VL  - 23
IS  - 3
SP  - 621-629
EP  - 621-629
PB  - Springer
SN  - 14396092
KW  - PCR
KW  - nDNA
KW  - Intron
KW  - Phylogenetic marker
KW  - Gastropods
UR  - https://doi.org/10.1007/s13127-022-00587-3
N2  - Progress in eupulmonate gastropod taxonomy is limited by absence of single- or low-copy nuclear DNA markers that provide species-scale insights. We detail here the single-copy intron 8 of the embryonic lethality and abnormal visual system gene (ELAVI8). High sequence conservation within flanking exons 8 and 9 allowed design of non-redundant primers that enable PCR amplification across a broad phylogenetic extent. Across the Eupulmonata and Hygrophila ELAVI8 product ranged from 602 to 802 base pairs in length. A multiple sequence alignment across 62 taxa, representing 36 genera and 12 major clades, showed 1296 sites with 865 variable positions. Typically, 2-10 base pair differences were noted between closely related species within a genus, with 74-200 bases differing between major infra-order clades. ELAVI8 maximum-likelihood trees showed essentially identical topologies at high levels of support compared to those created from concatenated ITS1 + 2 (within a genus) or 28S (across Eupulmonata and Hygrophila). ELAVI8 is superior to these two phylogenetic marker regions, however, because it (1) resolves phylogenetic pattern from species- to sub-cohort scales in a single amplicon, (2) was better able to resolve family- and deeper-clades at high support, (3) allows for outgroup rooting between genera, and (4) possesses no intercopy haplotype variability.
ER  -

NEKOLA, Jeffrey Clark, Markéta NOVÁKOVÁ, Michal HORSÁK a Coen M. ADEMA. ELAV Intron 8: a single-copy sequence marker for shallow to deep phylogeny in Eupulmonata Hasprunar \&{}amp; Huber, 1990 and Hygrophila Ferussac, 1822 (Gastropoda: Mollusca). \textit{Organisms Diversity and Evolution}. Springer, 2023, roč.~23, č.~3, s.~621-629. ISSN~1439-6092. Dostupné z: https://dx.doi.org/10.1007/s13127-022-00587-3.

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